Geometric model of quantum navigation during (anti-)search on a plane

A model of joint random walk of two agents on an infinite plane is considered. The agents possess no means of mutual classical communication, but have access to quantum entanglement resource which is used according to a pre-arranged protocol. Depending on the details of the protocol, an effective force of attraction or repulsion emerges between the two agents. The emergence of this force from quantum entanglement is interpreted in terms of spherical or hyperbolic geometries for attraction or repulsion, respectively.Comment: 4 pages, 3 figure

A major cellular substrate for protein kinases, annexin II, is a DNA-binding protein

AbstractWe have screened a human cDNA expression library in λgt11 for clones encoding Alu-binding proteins using direct binding of labeled Alu DNA to recombinant phage lysates fixed on a membrane, and isolated a clone 98% identical in sequence to the well-known substrate of protein kinases, annexin II, which was suggested earlier to play a role in transduction of mitogenic signals and DNA replication. A diagnostic property of annexins is their binding to phospholipids in the presence of calcium ions, and we have found that the interaction of proteins of human nuclear extracts with Alu subsequences is suppressed by Ca/phosphatidylserine liposomes, suggesting overlapping of Ca/phospholipid- and DNA-binding domains in annexin II

The theoretical DFT study of electronic structure of thin Si/SiO2 quantum nanodots and nanowires

The atomic and electronic structure of a set of proposed thin (1.6 nm in diameter) silicon/silica quantum nanodots and nanowires with narrow interface, as well as parent metastable silicon structures (1.2 nm in diameter), was studied in cluster and PBC approaches using B3LYP/6-31G* and PW PP LDA approximations. The total density of states (TDOS) of the smallest quasispherical silicon quantum dot (Si85) corresponds well to the TDOS of the bulk silicon. The elongated silicon nanodots and 1D nanowires demonstrate the metallic nature of the electronic structure. The surface oxidized layer opens the bandgap in the TDOS of the Si/SiO2 species. The top of the valence band and the bottom of conductivity band of the particles are formed by the silicon core derived states. The energy width of the bandgap is determined by the length of the Si/SiO2 clusters and demonstrates inverse dependence upon the size of the nanostructures. The theoretical data describes the size confinement effect in photoluminescence spectra of the silica embedded nanocrystalline silicon with high accuracy.Comment: 22 pages, 5 figures, 1 tabl

Stable maintenance of de novo assembled human artificial chromosomes in embryonic stem cells and their differentiated progeny in mice

De novo assembled alphoid(tetO)-type human artificial chromosomes (HACs) represent a novel promising generation of high capacity episomal vectors. Their function and persistence, and any adverse effects, in various cell types in live animals, have not, however, been explored. In this study we transferred the alphoid(tetO)-HAC into mouse ES cells and assessed whether the presence of this extra chromosome affects their pluripotent properties. Alphoid(tetO)-HAC-bearing ES cells were indistinguishable from their wild-type counterparts: they retained self-renewal potential and full capacity for multilineage differentiation during mouse development, whereas the HAC itself was mitotically and transcriptionally stable during this process. Our data provide the first example of fully synthetic DNA behaving like a normal chromosome in cells of living animals. It also opens a new perspective into functional genetic studies in laboratory animals as well as stem cell-based regenerative medicine

Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time‑dependent density functional theory

Active hydromedusan and ctenophore Ca2+-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460–470 nm, ctenophore photoproteins absorb at 437 nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein–substrate complex was optimized using a linear scaling quantum–mechanical method. Electronic excitations pertinent to the spectra of the 2-hydroperoxy adduct of coelenterazine were simulated with time-dependent density functional theory. The dihedral angle of 60° of the 6-(p-hydroxy)-phenyl group relative to the imidazopyrazinone core of 2-hydroperoxycoelenterazine molecule was found to be the key factor determining the absorption of ctenophore photoproteins at 437 nm. The residues relevant to binding of the substrate and its adopting the particular rotation were also identified

Computational approach to design of aptamers to the receptor binding domain of sars-cov-2

The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifications in order to increase the binding with the RBD. Thus, a new aptamer Apt25 was designed. The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets. Key words

Mathematical Modeling of a Solar Arrays Deploying Process at Ground Tests

This paper focuses on the creating of a mathematical model of a solar array deploying process during ground tests. Lagrange equation was used to obtain the math model. The distinctive feature of this mathematical model is the possibility of taking into account the gravity compensation system influence on the construction in the deploying process and the aerodynamic resistance during ground tests

Transfer of synthetic human chromosome into human induced pluripotent stem cells for biomedical applications

Alphoid(tetO)-type human artificial chromosome (HAC) has been recently synthetized as a novel class of gene delivery vectors for induced pluripotent stem cell (iPSC)-based tissue replacement therapeutic approach. This HAC vector was designed to deliver copies of genes into patients with genetic diseases caused by the loss of a particular gene function. The alphoid(tetO)-HAC vector has been successfully transferred into murine embryonic stem cells (ESCs) and maintained stably as an independent chromosome during the proliferation and differentiation of these cells. Human ESCs and iPSCs have significant differences in culturing conditions and pluripotency state in comparison with the murine naïve-type ESCs and iPSCs. To date, transferring alphoid(tetO)-HAC vector into human iPSCs (hiPSCs) remains a challenging task. In this study, we performed the microcell-mediated chromosome transfer (MMCT) of alphoid(tetO)-HAC expressing the green fluorescent protein into newly generated hiPSCs. We used a recently modified MMCT method that employs an envelope protein of amphotropic murine leukemia virus as a targeting cell fusion agent. Our data provide evidence that a totally artificial vector, alphoid(tetO)-HAC, can be transferred and maintained in human iPSCs as an independent autonomous chromosome without affecting pluripotent properties of the cells. These data also open new perspectives for implementing alphoid(tetO)-HAC as a gene therapy tool in future biomedical applications

Сравнительный анализ показателей качества лекарственного препарата альбумина человека с измененным стабилизирующим составом

Scientific relevance. The national and international human albumin preparations registered in the Russian Federation mainly differ in their excipient compositions. While all the international preparations of human albumin contain a mixture of sodium caprylate and N-acetyl-DL-tryptophan, the Russian ones contain only sodium caprylate. However, albumin stabilisation with sodium caprylate at high concentrations affects the ligand-binding properties of albumin. For this reason, as well as to achieve storage stability not only at temperatures of 2 °C to 8 °C but also   at room temperature, most international manufacturers have reduced the sodium caprylate content in albumin preparations and added N-acetyl-DL-tryptophan. This demonstrates the relevance of studying the quality of a new Russian human albumin preparation with a modified stabilising composition, including both sodium caprylate and N-acetyl-DL-tryptophan.Aim. The study aimed at comparing several quality attributes of the human albumin preparation with a modified stabilising composition with those of imported human albumin preparations.Materials and methods. The human albumin preparation with a modified stabilising composition was manufactured by fractionation from donor plasma meeting the requirements of monograph FS.3.3.2.0001.19 of the State Pharmacopoeia of the Russian Federation edition XIV. The quality control was in line with the monograph on human albumin (FS.3.3.2.0006.18), and statistical analysis was conducted in Microsoft Excel in accordance with the general chapter on statistical analysis (OFS.1.1.0013.15).Results. The study preparation complied with the requirements specified in monograph FS.3.3.2.0006.18. All the manufactured batches were clear, thermostable, sterile, and non-pyrogenic. The prekallikrein activator levels were low (below 1 IU/mL). The aluminium content varied from 30.36±10.39 µg/L to 50.22±6.94 µg/L. The study preparation contained sodium ions at a concentration from 127.44±10.46 mmol/L to 145.59±7.32 mmol/L and less than 0.01 mmol/g of potassium ions. The osmolarity exceeded 240 mOsm/L. The content of α- and β-globulins  ranged  from  1.79±0.06%  to  2.24±0.20%.  The  study  preparation  had  a  pH  level  of 6.9 to 7.2. The concentrations of polymers and aggregates did not exceed 0.5%.Conclusions. The quality attributes studied suggest that the human albumin preparation with   a modified stabilising composition is comparable to its international counterparts and that it meets Russian and European pharmacopoeial standards.Актуальность. Зарубежные лекарственные препараты альбумина человека, зарегистрированные в Российской Федерации, отличаются от отечественных главным образом по составу вспомогательных веществ. Все иностранные препараты альбумина содержат смесь вспомогательных веществ — натрия каприлата и N-ацетил-DL-триптофана; отечественные — только натрия каприлат. Однако стабилизация раствора альбумина натрия каприлатом в высоких концентрациях приводит к ухудшению его лигандсвязывающих свойств. По этой причине, а также для достижения стабильности препаратов при хранении не только при температуре от 2 до 8 °C, но и при комнатной температуре, большинство зарубежных производителей изменили состав препарата альбумина путем снижения содержания натрия каприлата и дополнительного введения N-ацетил-DL-триптофана. В связи с этим актуальным представляется изучение показателей качества разработанного отечественного препарата альбумина человека с измененным стабилизирующим составом, содержащим оба указанных компонента.Цель. Анализ показателей качества препарата альбумина человека с измененным стабилизирующим составом в сравнении с зарубежными лекарственными средствами.Материалы и методы. Активной фармацевтической субстанцией для получения препарата альбумина человека с измененным стабилизирующим составом служила плазма крови доноров, соответствующая требованиям Государственной фармакопеи Российской Федерации XIV изд. (ГФ РФ XIV) ФС.3.3.2.0001.19. Препарат получали методом фракционирования белков плазмы крови. Контроль показателей качества препарата осуществляли в соответствии с требованиями  ФС.3.3.2.0006.18.  Статистическую обработку проводили с помощью программы Microsoft Excel в соответствии с ОФС.1.1.0013.15.Результаты. Показано соответствие показателей качества исследуемого препарата установленным требованиям  ФС.3.3.2.0006.18. В ходе исследований   установлено,  что изготовленные серии  препарата были прозрачными,  термостабильными, стерильными  и апирогенными; имели низкий уровень активатора прекалликреина — менее 1 МЕ/мл; содержание алюминия было в диапазоне от 30,36±10,39 до  50,22±6,94  мкг/л;  натрий-иона — от 127,44±10,46 до 145,59±7,32 ммоль/л; калий-иона — менее 0,01 ммоль/г; осмолярность — более 240 мОсм/л. Препарат содержал от 1,79±0,06 до 2,24±0,20% примесей других белков  (α- и β-глобулинов); показатель рН был в диапазоне от 6,9 до 7,2;  концентрация полимеров    и агрегатов не превышала 0,5%.Выводы. По изученным показателям качества препарат альбумина человека  с  измененным стабилизирующим составом был сопоставим с зарубежными аналогами и соответствовал требованиям ГФ РФ XIV и Европейской фармакопеи